Sequence Alignment by Blast issue
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Entering edit mode
5 months ago
sara • 0

I'm trying to make sequence alignment using blast, however, it keeps getting this error

Warning: Sequence contains no data Sequence contains no data Warning: Sequence contains no data Warning: Sequence contains no data Warning: Sequence contains no data Warning: Sequence contains no data Warning: Sequence contains no data Warning: Sequence contains no data Warning: Sequence contains no data Warning: Sequence contains no data Warning: Sequence contains no data Warning:

That's an example of my sample data file:

>SRR12802808.400000 400000 length=2907  TTGGTATGCTTCGTTCAGTTACGTACTACTTGCCTGTCGCTCTATCTTCGGCGTCTGCTTGGGTGTTTAACCTTGCTTAACAAACAAGAAACAAGGGACTCTCTAAAACCAAAGTCTCACTAAGTTTAAAACACCCAAACAGACATATAATATCAGCACCAACAGAAAGCAATACATGCTTGC +SRR12802808.400000 400000 length=2907  %'4*,,-&.0:53496140900.8.1/,),,.67783/01324664720834541/.7/886///:8011*0-+*+5;7.28;8;1;8/''((61//*%#0*65;42,/866487/:///9::/&07(0-5-.  and aligning it with chromosome 22 Blast Alignment • 351 views ADD COMMENT 1 Entering edit mode 5 months ago GenoMax 117k You can't use fastq format data for blast searches. You will need to convert this data to fasta format. You can use reformat.sh from BBMap suite or seqtk fasta for this conversion. ADD COMMENT 0 Entering edit mode What is the differance between the two formats ? ADD REPLY 1 Entering edit mode Fasta format is simply as follows (> followed by identifier then sequence on second line): >SRR12802808.400000 400000 length=2907 TTGGTATGCTTCGTTCAGTTACGTACTACTTGC  Fastq format includes a per base quality score (see more in Wiki article). There are 4 lines per sequence record. @SRR12802808.400000 400000 length=2907 TTGGTATGCTTCGTTCAGTTACGTACTACTTGCCT +SRR12802808.400000 400000 length=2907 %'4*,,-&.0:53496140900.8.1/,),,.67

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I got it now, thank you !